Soil generally serves as both sink and source for atmospheric CO₂, and plays a crucial role in maintaining carbon balance on the global scale, and mitigating the greenhouse effect. Mechanisms for interaction and combination between climate change and soil carbon pool have long been a hot spot and a hard nut to crack for the academic circle. Although extensive studies have been done on the subject at community-ecosystem, and regional-global scales, little has been reported about mechanisms of the variation of climate factors affecting chemical structure of the soil organic carbon pool (SOC) at the molecular scale. This review summarizes recent works on changes in climate factors and the changes in environmental and ecological factors they trigger and their relationships with molecular structure of the soil organic carbon pool. Climate warming not only changes characteristics of the sources of SOC from plant tissues, and significantly increases the content of cutin, a component of leaf epidermis, but also keeps relatively unchanged or declining the major components of SOC, such as carbohydrate, lignin, suberin and the like. Meanwhile, warming also accelerates decomposition of lignin and some other carbon components, promotes decomposition of aliphatic compounds, cutin and cyclic compounds and enhances soil microbiota in activity, thus leading to accumulation of plant-sourced alkyl-structured and/or microbe-sourced organic matter. Changes in soil hydrological regime also alter characteristics of the functional groups of soil organic carbon. For instance, drainage or drought triggers acceleration of decomposition of organic matter mineralization, thus increasing C=O bonds in soil; and fluctuation of soil water table controls chemical structure of the organic matter by affecting Fe form in the soil. Vegetation succession changes sources of soil organic matter due to difference between plant residues in inherent resistance to decomposition, and consequently alters properties of the soil organic carbon in the end. In the same climate zone, soils covered with various predominant vegetations are often characterized by remarkable differences in molecular structure of soil organic matter. Soil fauna and microorganisms, which are both ecological factors closely related to climate change, also alter properties of the plant residues in soil, promote decomposition of lipids, lignin and saccharides, and form different biomarkers. However, still not much has been done on how soil fauna and microbes alter molecular structure of soil organic matter. Stability of SOC is closely related to molecular structure of soil organic matter. Generally, SOC are more stable in the soil where contents of aromatic and O-alkyl compounds are high. In the soil the youngest fraction of carbon (formed in the past 107 years) usually features more aromatic compounds and low ratios of O-alkyl carbon to aromatic carbon, while the oldest fraction of carbon (over 1000 years) does less compounds and O-alkyl carbon. However, lignin is not so stable as previously expected facing climate warming. In the future, more researches should be done with stresses on special biomarkers and their ecological meaning, effect and mechanism of biota regulating molecular transformation processes of SOC, combined mechanisms of large-scaled environmental/ecological process and transformation of molecular structure of the carbon pool, and techniques to identify and interpret new molecular structures of SOC.